Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle
Abstract
:1. Introduction
2. Materials and Methods
2.1. Microarray Data Pre-Processing and Statistical Analysis
2.2. Network Module Creation Using the Integration of Protein–Protein Interactions (PPIs)
2.3. miRNAs, Biological Processes, and Pathway Analysis of DEGs
2.4. Relevance Network Design
3. Results
3.1. DEGs Identification and PPI Analysis
3.2. Network Analysis
3.3. Biological Processes, Pathway Analysis, and miRNA Identification
4. Discussion
4.1. Hub Genes Related to Milk Production
4.2. miRNAs Related to Milk Production
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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No. | Genes | p-Value |
---|---|---|
Cluster 1 | GUF1, MRPS14, MRPL9, RPS27, YKT6, RAB6B, VPS54, VPS33B | 5.8 × 10−9 |
Cluster 2 | GAPDH, KDR, CSF1, PYGM, GUSB, CXCR4, FGF18, FABP4, GDF10, BMP10, SMAD6 | 3.4 × 10−10 |
Cluster 3 | PPP2CA, PRKCA, CACNG4, MAPK7, CCNI, BAK1, ANKLE2, PRKCA | 3.26 × 10−7 |
Cluster 4 | PRKAA1, AMDHD2, GNPDA2, PGM3, PGM2L1, PFKFB1, PDE6G | 0.000151 |
Gene | Gene Name | Expression Log FC | Degree | Betweenness | Closeness |
---|---|---|---|---|---|
GAPDH | glyceraldehyde-3-phosphate dehydrogenase | −1.07139 | 22 | 4384.83 | 0.074 |
KDR | Kinase insert domain receptor | −0.99096 | 8 | 539.66 | 0.070 |
CSF1 | Colony-stimulating factor1 | −0.49033 | 8 | 180.5 | 0.070 |
PYGM | phosphorylase, glycogen, muscle associated | −0.4587 | 6 | 2199.0 | 0.072 |
RET | Ret proto-oncogene | −0.39795 | 6 | 397.33 | 0.071 |
PPP2CA | Protein phosphatase 2 catalytic subunit alpha | 0.66955 | 5 | 763.0 | 0.068 |
GUSB | Glucuronidase beta | 0.371806 | 5 | 272.33 | 0.070 |
PRKCA | Protein kinase C alpha | −0.33072 | 5 | 418.66 | 0.068 |
Biological Activity Analysis of Clustered Genes | |
---|---|
Cluster 1 | Translation, mitochondrial translational elongation, mitochondrial translational initiation, protein transport. |
Cluster 2 | BMP signalling pathway, regulation of MAPK cascade, fat cell differentiation, carbohydrate metabolic process, cell development, SMAD protein signal transduction, positive regulation of ERK1 and ERK2 cascade, and positive regulation of gene expression. |
Cluster 3 | Regulation of cell cycle, cell proliferation, calcium ion transmembrane transport, peptidyl-serine phosphorylation, and positive regulation of calcium ion transport into cytosol. |
Cluster 4 | Carbohydrate metabolic process, N-acetylglucosamine metabolic process, N-acetylglucosamine catabolic process, N-acetylneuraminate catabolic process, glycogen catabolic process, and lipid biosynthetic process. |
Pathway Analysis of Clustered Gene | |
---|---|
Cluster 1 | Ribosome, SNARE interactions in vesicular transport. |
Cluster 2 | Rap1 signalling pathway, Ras signalling pathway, Chemokine signalling pathway, PI3K-Akt signalling pathway. |
Cluster 3 | Protein processing in endoplasmic reticulum, MAPK signalling pathway, ErbB signalling pathway, Ras signalling pathway, Rap1 signalling pathway, Calcium signalling pathway, HIF-1 signalling pathway. |
Cluster 4 | Amino sugar and nucleotide sugar metabolism, Glucagon signalling pathway, AMPK signalling pathway. |
Target Genes | miRNAs |
---|---|
RET | bta-miR-141, bta-miR-181a, bta-miR-194, bta-miR-2410, bta-miR-29b, bta-miR-760-3p, bta-miR-7863 |
CXCR4 | bta-miR-2344 |
GAPDH | bta-miR-2340 |
CSF1 | bta-miR-10b, bta-miR-204, bta-miR-214, bta-miR-24, bta-miR-375, bta-miR-665, bta-miR-760-3p, bta-miR-7863 |
KDR | bta-miR-375, bta-miR-2320-5p |
VPS54 | bta-miR-146a, bta-miR-22-3p, bta-miR-2413, bta-miR-31 |
RAB6B | bta-miR-149-5p, bta-miR-21-3p, bta-miR-2357, bta-miR-29b, bta-miR-27a-5p, bta-miR-431, bta-miR-491, bta-miR-541, bta-miR-760-3p |
VPS33B | bta-miR-183, bta-miR-1247-3p, bta-miR-7863 |
YKT6 | bta-miR-197, bta-miR-500, bta-miR-133a, bta-miR-133b |
MRPL9 | bta-miR-370, bta-miR-665 |
GUF1 | bta-miR-10b, bta-miR-204, bta-miR-214, bta-miR-24, bta-miR-375, bta-miR-665, bta-miR-760-3p, bta-miR-7863 |
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Roudbari, Z.; Mokhtari, M.; Ebrahimpour Gorji, A.; Sadkowski, T.; Sadr, A.S.; Shirali, M. Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle. Genes 2023, 14, 2105. https://doi.org/10.3390/genes14112105
Roudbari Z, Mokhtari M, Ebrahimpour Gorji A, Sadkowski T, Sadr AS, Shirali M. Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle. Genes. 2023; 14(11):2105. https://doi.org/10.3390/genes14112105
Chicago/Turabian StyleRoudbari, Zahra, Morteza Mokhtari, Abdolvahab Ebrahimpour Gorji, Tomasz Sadkowski, Ayeh Sadat Sadr, and Masoud Shirali. 2023. "Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle" Genes 14, no. 11: 2105. https://doi.org/10.3390/genes14112105
APA StyleRoudbari, Z., Mokhtari, M., Ebrahimpour Gorji, A., Sadkowski, T., Sadr, A. S., & Shirali, M. (2023). Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle. Genes, 14(11), 2105. https://doi.org/10.3390/genes14112105